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From the Unix side, your best bet is to use strace/truss on the server process to check which (if any) syscalls are hanging. Someone else will be along shortly with suggestions from the MySQL side :)
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tblPhilOct 29 '12 at 13:40

Is the profiling flag automatically unset when I leave the MySQL session?
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Adam MatanOct 29 '12 at 14:18

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Yeah, it's a session variable, and it's default is 'off' so it will be off for your next session.
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Derek DowneyOct 29 '12 at 14:19

Thanks a bunch, it's a cool tool. Added the result to my question.
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Adam MatanOct 29 '12 at 14:21

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@AdamMatan not sure if you read the profiling documentation, but there are other flags for showing profile of the query CPU, BLOCK IO etc that might help you on the 'creating table' stage.
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Derek DowneyOct 29 '12 at 15:05